3kv4

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==Structure of PHF8 in complex with histone H3==
==Structure of PHF8 in complex with histone H3==
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<StructureSection load='3kv4' size='340' side='right' caption='[[3kv4]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
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<StructureSection load='3kv4' size='340' side='right'caption='[[3kv4]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3kv4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KV4 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3kv4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KV4 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.19&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kv5|3kv5]], [[3kv6|3kv6]], [[3kv9|3kv9]], [[3kva|3kva]], [[3kvb|3kvb]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kv4 OCA], [https://pdbe.org/3kv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kv4 RCSB], [https://www.ebi.ac.uk/pdbsum/3kv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kv4 ProSAT]</span></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KIAA1111, PHF8, ZNF422 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kv4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kv4 RCSB], [http://www.ebi.ac.uk/pdbsum/3kv4 PDBsum]</span></td></tr>
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</table>
</table>
== Disease ==
== Disease ==
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[[http://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN]] Defects in PHF8 are the cause of mental retardation syndromic X-linked Siderius type (MRXSSD) [MIM:[http://omim.org/entry/300263 300263]]. A disorder characterized by mild to borderline mental retardation with or without cleft lip/cleft palate.<ref>PMID:20548336</ref> <ref>PMID:20346720</ref> <ref>PMID:20421419</ref> <ref>PMID:20208542</ref> <ref>PMID:20622853</ref> <ref>PMID:20622854</ref> <ref>PMID:20101266</ref> <ref>PMID:16199551</ref> <ref>PMID:17661819</ref>
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[https://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN] Defects in PHF8 are the cause of mental retardation syndromic X-linked Siderius type (MRXSSD) [MIM:[https://omim.org/entry/300263 300263]. A disorder characterized by mild to borderline mental retardation with or without cleft lip/cleft palate.<ref>PMID:20548336</ref> <ref>PMID:20346720</ref> <ref>PMID:20421419</ref> <ref>PMID:20208542</ref> <ref>PMID:20622853</ref> <ref>PMID:20622854</ref> <ref>PMID:20101266</ref> <ref>PMID:16199551</ref> <ref>PMID:17661819</ref>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN]] Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20' residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3.<ref>PMID:20531378</ref> <ref>PMID:20548336</ref> <ref>PMID:19843542</ref> <ref>PMID:20346720</ref> <ref>PMID:20421419</ref> <ref>PMID:20208542</ref> <ref>PMID:20622853</ref> <ref>PMID:20622854</ref> <ref>PMID:20101266</ref> <ref>PMID:20023638</ref> [[http://www.uniprot.org/uniprot/H3L_HUMAN H3L_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.<ref>PMID:21274551</ref>
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[https://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN] Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20' residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3.<ref>PMID:20531378</ref> <ref>PMID:20548336</ref> <ref>PMID:19843542</ref> <ref>PMID:20346720</ref> <ref>PMID:20421419</ref> <ref>PMID:20208542</ref> <ref>PMID:20622853</ref> <ref>PMID:20622854</ref> <ref>PMID:20101266</ref> <ref>PMID:20023638</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kv4_consurf.spt"</scriptWhenChecked>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kv4_consurf.spt"</scriptWhenChecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kv4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
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<div class="pdbe-citations 3kv4" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Cheng, X]]
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[[Category: Large Structures]]
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[[Category: Horton, J R]]
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[[Category: Cheng X]]
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[[Category: Qi, H H]]
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[[Category: Horton JR]]
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[[Category: Shi, Y]]
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[[Category: Qi HH]]
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[[Category: Upadhyay, A K]]
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[[Category: Shi Y]]
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[[Category: Zhang, X]]
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[[Category: Upadhyay AK]]
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[[Category: Covalent histone modification]]
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[[Category: Zhang X]]
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[[Category: Epigenetic]]
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[[Category: H3k4me3 binding protein]]
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[[Category: Histone code]]
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[[Category: Jumonji demethylase]]
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[[Category: Mental retardation]]
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[[Category: Metal-binding]]
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[[Category: Transferase]]
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[[Category: Zinc-finger]]
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Current revision

Structure of PHF8 in complex with histone H3

PDB ID 3kv4

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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